You are here

Slice Timing

Submitted by Bin Lu on Mon, 10/16/2017 - 02:48

Most fMRI data are acquired using two-dimensional pulse sequences that acquire images one slice at a time, thus all slices are acquired at different time within a repeat time (TR). Timing differences are especially problematic for longer TR. Hence the differences in image acquisition time between slices need to be corrected. The number of slices, slice order and reference slice need to be specified, then DPARSF will do slice timing by calling functions in SPM.

For batch mode, The slice order type could be specified for each participant into SliceOrderInfo.tsv (under working directory) file, thus allow different slice timing correction for different participants. Please specify Slice Number as 0 in DPARSFA GUI.

Within SliceOrderInfor.tsv, the first column is Subject ID, and the second column is Slice Order Type. The third column (if available) is the Slice Order Type for Session 2.

SA: sequential ascending

SD: sequential descending

IA: interleaved ascending

ID: interleaved descending

IA2: interleaved ascending, for SIEMENS scanner with even number of slices. Scanning of 2,4,6,... and then 1,3,5,... i.e., [2:2:SliceNumber,1:2:SliceNumber]

ID2: interleaved descending, for SIEMENS scanner with even number of slices. Scanning of [SliceNumber-1:-2:1,SliceNumber:-2:1].

Please see {DPARSF}/Docs/SliceOrderInfo.tsv for a sample file. Also, please see Yan et al., 2013 Table 3 for a sample of FCP data (although IA2 and ID2 were not defined in that table.)

Forums:

For batch mode, The slice order type could be specified for each participant into SliceOrderInfo.tsv (under working directory) file, thus allow different slice timing correction for different participants. Please specify Slice Number as 0 in DPARSFA GUI.

Within SliceOrderInfor.tsv, the first column is Subject ID, and the second column is Slice Order Type. The third column (if available) is the Slice Order Type for Session 2.

SA: sequential ascending

SD: sequential descending

IA: interleaved ascending

ID: interleaved descending

IA2: interleaved ascending, for SIEMENS scanner with even number of slices. Scanning of 2,4,6,... and then 1,3,5,... i.e., [2:2:SliceNumber,1:2:SliceNumber]

ID2: interleaved descending, for SIEMENS scanner with even number of slices. Scanning of [SliceNumber-1:-2:1,SliceNumber:-2:1].

Taking the SliceOrderInfo.tsv for example.

Put the file under /Subjects/*.tsv

In DPARSF GUI:

Slice number as 0 (if "0", detect automatically right?)

Slice order = ?

Reference slice as 0 (if "0", detect automatically right?)

By the way, where could I get the slice number and order type information for ABIDE data sets?